import more Compartment metadata, mainly the sizes

src/readsbml.jl

@@ -35,6 +35,45 @@ function get_optional_string(x::VPtr, fn_sym)::Maybe{String}
     end
 end
 
+"""
+    get_optional_bool(x::VPtr, is_sym, get_sym)::Maybe{Bool}
+
+Helper for getting out boolean flags.
+"""
+function get_optional_bool(x::VPtr, is_sym, get_sym)::Maybe{Bool}
+    if ccall(sbml(is_sym), Cint, (VPtr,), x) != 0
+        return ccall(sbml(get_sym), Cint, (VPtr,), x) != 0
+    else
+        return nothing
+    end
+end
+
+"""
+    get_optional_int(x::VPtr, is_sym, get_sym)::Maybe{UInt}
+
+Helper for getting out unsigned integers.
+"""
+function get_optional_int(x::VPtr, is_sym, get_sym)::Maybe{Int}
+    if ccall(sbml(is_sym), Cint, (VPtr,), x) != 0
+        return ccall(sbml(get_sym), Cint, (VPtr,), x)
+    else
+        return nothing
+    end
+end
+
+"""
+    get_optional_double(x::VPtr, is_sym, get_sym)::Maybe{Float64}
+
+Helper for getting out C doubles aka Float64s.
+"""
+function get_optional_double(x::VPtr, is_sym, get_sym)::Maybe{Float64}
+    if ccall(sbml(is_sym), Cint, (VPtr,), x) != 0
+        return ccall(sbml(get_sym), Cdouble, (VPtr,), x)
+    else
+        return nothing
+    end
+end
+
 """
     function readSBML(fn::String)::Model
 
@@ -143,12 +182,24 @@ function extractModel(mdl::VPtr)::Model
     end
 
     # parse out compartment names
-    compartments = [
-        get_string(
-            ccall(sbml(:Model_getCompartment), VPtr, (VPtr, Cuint), mdl, i - 1),
-            :Compartment_getId,
-        ) for i = 1:ccall(sbml(:Model_getNumCompartments), Cuint, (VPtr,), mdl)
-    ]
+    compartments = Dict{String,Compartment}()
+    for i = 1:ccall(sbml(:Model_getNumCompartments), Cuint, (VPtr,), mdl)
+        co = ccall(sbml(:Model_getCompartment), VPtr, (VPtr, Cuint), mdl, i - 1)
+
+        compartments[get_string(co, :Compartment_getId)] = Compartment(
+            get_optional_string(co, :Compartment_getName),
+            get_optional_bool(co, :Compartment_isSetConstant, :Compartment_getConstant),
+            get_optional_int(
+                co,
+                :Compartment_isSetSpatialDimensions,
+                :Compartment_getSpatialDimensions,
+            ),
+            get_optional_double(co, :Compartment_isSetSize, :Compartment_getSize),
+            get_optional_string(co, :Compartment_getUnits),
+            get_notes(co),
+            get_annotation(co),
+        )
+    end
 
     # parse out species
     species = Dict{String,Species}()
@@ -183,7 +234,11 @@ function extractModel(mdl::VPtr)::Model
             formula,
             charge,
             ia,
-            ccall(sbml(:Species_getHasOnlySubstanceUnits), Cint, (VPtr,), sp) != 0,
+            get_optional_bool(
+                sp,
+                :Species_isSetHasOnlySubstanceUnits,
+                :Species_getHasOnlySubstanceUnits,
+            ),
             get_notes(sp),
             get_annotation(sp),
         )

src/structs.jl

@@ -90,6 +90,20 @@ struct MathLambda <: Math
     body::Math
 end
 
+"""
+SBML Compartment with sizing information.
+"""
+struct Compartment
+    name::Maybe{String}
+    constant::Maybe{Bool}
+    spatial_dimensions::Maybe{Int}
+    size::Maybe{Float64}
+    units::Maybe{String}
+    notes::Maybe{String}
+    annotation::Maybe{String}
+    Compartment(na, c, sd, s, u, no = nothing, an = nothing) = new(na, c, sd, s, u, no, an)
+end
+
 """
 Reaction with stoichiometry that assigns reactants and products their relative
 consumption/production rates (accessible in field `stoichiometry`), lower/upper
@@ -118,7 +132,7 @@ struct Species
     formula::Maybe{String}
     charge::Maybe{Int}
     initial_amount::Maybe{Tuple{Float64,String}}
-    only_substance_units::Bool
+    only_substance_units::Maybe{Bool}
     notes::Maybe{String}
     annotation::Maybe{String}
     Species(na, co, f, ch, ia, osu, no = nothing, a = nothing) =
@@ -157,7 +171,7 @@ objects.
 struct Model
     parameters::Dict{String,Float64}
     units::Dict{String,Vector{UnitPart}}
-    compartments::Vector{String}
+    compartments::Dict{String,Compartment}
     species::Dict{String,Species}
     reactions::Dict{String,Reaction}
     gene_products::Dict{String,GeneProduct}